Biology subjects

Chan, K. O.

Publications and source records attributed to Chan, K. O..

9 recordsLinked to original sources

bioRxiv2025

Sampling bias obscures biodiversity patterns, reveals data gaps in priority conservation areas: a call for improved documentation

Where and how species are sampled can shape biodiversity knowledge, spatial patterns, and data-driven conservation. In megadiverse regions of the Global South, sampling remains uneven, and available data often lack synthesis needed to assess spatial heterogeneity in recorded biodiversity for conservation planning. This limitation is also evident in areas designated for biodiversity conservation. We examine this in the Philippines, where long-term research effort and policy development have supported expansion of conservation-relevant areas (hereafter "Philippine conservation-relevant areas" or PCAs). Using over a century of digitally accessible species occurrence records compiled and manually curated, we analyzed the country-wide spatial distribution of observed amphibian and squamate reptile species richness. We further tested whether observed richness across PCAs is associated with area, topographic relief, and sampling effort, and whether these relationships differ between protected and conserved areas (with management or governance schemes) and key biodiversity areas (unmanaged but priority areas for conservation). Results show strong spatial heterogeneity in occurrence records, with preserved specimens comprising 92% of all records and strongly influencing observed richness patterns. Citizen-science data tend to reinforce already well-sampled regions, whereas literature-derived records provide additional coverage in comparatively undersampled areas. PCAs show variable representation in the dataset, with observed richness and sampling effort generally increasing with area. However, this richness-area relationship weakens with increasing topographic relief. Differences in predictor-richness relationships between PCA types are also evident, with stronger area and sampling effects in protected and conserved areas and a relatively stronger elevational effect in key biodiversity areas. Notably, several high-richness areas occur outside formally designated protected areas. These results highlight uneven biodiversity data coverage and suggest that observed richness patterns may reflect both sampling structure and spatial variation. We emphasize integrating multiple biodiversity data sources and identifying undersampled regions to improve future biodiversity assessments.

ecology↗

bioRxiv2024

The Amphibian Genomics Consortium: advancing genomic and genetic resources for amphibian research and conservation

Amphibians represent a diverse group of tetrapods, marked by deep divergence times between their three systematic orders and families. Studying amphibian biology through the genomics lens increases our understanding of the features of this animal class and that of other terrestrial vertebrates. The need for amphibian genomic resources is more urgent than ever due to the increasing threats to this group. Amphibians are one of the most imperiled taxonomic groups, with approximately 41% of species threatened with extinction due to habitat loss, changes in land use patterns, disease, climate change, and their synergistic effects. Amphibian genomic resources have provided a better understanding of ontogenetic diversity, tissue regeneration, diverse life history and reproductive modes, anti-predator strategies, and resilience and adaptive responses. They also serve as essential models for studying broad genomic traits, such as evolutionary genome expansions and contractions, as they exhibit the widest range of genome sizes among all animal taxa and possess multiple mechanisms of genetic sex determination. Despite these features, genome sequencing of amphibians has significantly lagged behind that of other vertebrates, primarily due to the challenges of assembling their large, repeat-rich genomes and the relative lack of societal support. The emergence of long-read sequencing technologies, combined with advanced molecular and computational techniques that improve scaffolding and reduce computational workloads, is now making it possible to address some of these challenges. To promote and accelerate the production and use of amphibian genomics research through international coordination and collaboration, we launched the Amphibian Genomics Consortium (AGC, https://mvs.unimelb.edu.au/amphibian-genomics-consortium) in early 2023. This burgeoning community already has more than 282 members from 41 countries. The AGC aims to leverage the diverse capabilities of its members to advance genomic resources for amphibians and bridge the implementation gap between biologists, bioinformaticians, and conservation practitioners. Here we evaluate the state of the field of amphibian genomics, highlight previous studies, present challenges to overcome, and call on the research and conservation communities to unite as part of the AGC to enable amphibian genomics research to "leap" to the next level.

genomics↗

bioRxiv2021

Patterns and Progress of Peninsular Malaysia's Amphibian Research in the 21st Century (2000-2020)

In this study, we review the status, patterns, and progress of Peninsular Malaysias amphibian research in the 21st century with the main goal of identifying areas for improvement that can help focus and prioritize future research initiatives. Between 2000-2020 we found 130 publications that can be broadly categorized into four groups: 1) checklists and biodiversity; 2) new species and taxonomy; 3) ecology and natural history; and 4) evolution and phylogenetics. An average of 6.5 papers was published per year and although the number of papers fluctuated, there was a significant upward trend in the number of papers published. Almost half (49%) of all papers published comprised checklists and biodiversity-related papers. This was followed by new species and taxonomy (25%, 33 papers), evolution and phylogenetics (14%, 18 papers), and ecology and natural history (12%, 16 papers). Amphibian research was conducted most frequently in the states of Kedah, Pahang, and Perak, and most infrequently in the states of Malacca, Negeri Sembilan, Selangor/Kuala Lumpur, Perlis, and Kelantan. Despite being a megadiverse country and a biodiversity hotspot, not a single conservation-centric paper has ever been published on Peninsular Malaysian amphibians, highlighting the urgent need for future research to focus on conservation.

scientific communication and education↗

bioRxiv2021

Correcting for Body Size Variation in Morphometric Analysis

Using an allometric growth model to correct for body size variation has been known for many decades to be superior to several other widely used methods such as ratios, analysis of covariance, principal components analysis, and residual analysis. However, this technique remains relatively obscure and rarely applied. We optimize the implementation of this method through a newly developed and easy-to-use R package GroupStruct and use empirical datasets to test its relative efficacy compared to several commonly used methods. Our results demonstrate the superiority of the allometric method and highlights the negative impacts of applying improper body size correction methods.

zoology↗

bioRxiv2021

Integrating spatial, phylogenetic, and threat assessment data from frogs and lizards to identify areas for conservation priorities in Peninsular Malaysia

Malaysia is recognized as a megadiverse country and biodiversity hotspot, which necessitates sufficient levels of habitat protection and effective conservation management. However, conservation planning in Malaysia has hitherto relied largely on species distribution data without taking into account the rich evolutionary history of taxa. This represents the first study that integrates spatial and evolutionary approaches to identify important centers of diversity, endemism, and bioregionalization that can be earmarked for conservation priorities in Peninsular Malaysia. Using georeferenced species occurrences, comprehensive phylogenies, and threat assessments of frogs and lizards, we employed a spatial phylogenetics framework that incorporates various diversity metrics including weighted endemism, phylogenetic diversity, phylogenetic endemism, and evolutionary distinctiveness and global endangerment. Ten areas of high conservation value were identified via the intersection of these metrics--northern Perlis, Langkawi Geopark, southern Bintang range, Cameron Highlands, Frasers Hill, Benom-Krau complex, Selangor-Genting complex, Endau-Rompin National Park, Seribuat Archipelago (Tioman and Pemanggil Islands), and southern Johor. Of these, Cameron Highlands requires the highest conservation priority based on severe environmental degradation, inadequately protected areas, and high numbers of endangered and evolutionary distinct species. Other areas, especially in the northwestern (states of Kedah and Penang) and northeastern regions (states of Kelantan) were not only identified as areas of high conservation value but also areas of biogeographic importance. Taken together, frogs and lizards demonstrate distinct east-west and north-south patterns of bioregionalization that are largely modulated by mountain ranges. Article Impact StatementThe first study to use a spatial phylogenetic approach to identify areas for conservation priorities in Malaysia

ecology↗

bioRxiv2019

Species delimitation in the grey zone: introgression obfuscates phylogenetic inference and species boundaries in a cryptic frog complex (Ranidae: Pulchrana picturata)

As molecular methods continue to elucidate genetic structure at increasingly finer resolutions, delimiting species in the grey zone of the speciation continuum is becoming more relevant in biodiversity research, especially in under-studied biodiversity hotspots such as Southeast Asia where new species are being described at an unprecedented rate. Obvious species at both ends of the speciation continuum have mostly been described and attention is now turning towards the \"grey zone:\" an intermediate stage in which species criteria are in conflict and boundaries between populations and species are less clear. This study demonstrates that widely-used criteria (phylogenetic placement, genetic divergence, phylogeny- and distance-based species delimitation methods) can overestimate species diversity/boundaries when introgression is present. However, a comprehensive species delimitation framework that considers spatial and genetic population structure, introgression, and the use of species delimitation methods based on parameter estimation, can provide a more accurate characterization of species boundaries in this grey zone. We applied this approach to a group of Southeast Asian frogs from the Pulchrana picturata Complex that exhibits continuous morphological variation and high genetic divergences. Results showed that introgression was rampant among Bornean populations, which led to phylogenetic discordance and an overestimation of species. We suspect that our results do not form an isolated case; and that introgression among cryptic populations, occurring continuously across a wide geographic area (e.g., the topographically complex island of Borneo, and Earths major continents), may be more common than previously thought.

evolutionary biology↗

bioRxiv2019

Exons, Introns, and UCEs Reveal Conflicting Phylogenomic Signals in a Rapid Radiation of Frogs (Ranidae: Hylarana)

The manuscript titled \"Exons, Introns, and UCEs Reveal Conflicting Phylogenomic Signals in a Rapid Radiation of Frogs (Ranidae: Hylarana)\" has been withdrawn from BioRxiv temporarily. The manuscript has been withdrawn because it utilizes a new protocol for data collection, which has yet not been published. Once the paper describing the new method becomes available for circulation, this manuscript will be resubmitted to BioRxiv. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

evolutionary biology↗

bioRxiv2019

Phylogeography and Molecular Species Delimitation Reveal Cryptic and Incipient Speciation in Synchronous Flashing Fireflies (Coleoptera: Lampyridae) of Southeast Asia

Synchronous flashing fireflies of the genus Pteroptyx are ubiquitous throughout Southeast Asia, yet, knowledge on its biodiversity and evolutionary history remains lacking. Recent studies have revealed notable population-level phylogeographic structure within the P. tener and P. bearni groups in Malaysia, suggesting that cryptic species may exist. Additionally, the close morphological and genetic affinity of the recently described species P. balingiana to P. malaccae has raised questions about its validity. In this study, we assembled the most densely sampled genetic dataset on Pteroptyx to-date to estimate a comprehensive phylogeny using mitochondrial and nuclear DNA and subsequently implemented a suite of distance-, phylogeny-, and coalescent-based species delimitation methods to characterize species boundaries within the P. tener, P. bearni, and P. balingiana/P. malaccae groups. Using a total evidence approach from multiple lines of evidence, we showed that populations of P. tener along the west coast of Peninsular Malaysia are sufficiently divergent from populations from the east coast and Borneo to warrant specific recognition, despite the absence of morphological differentiation. Conversely, divergence of P. bearni from Borneo and eastern Peninsular Malaysia, as well as P. balingiana from P. malaccae were modest and their distinction as separate species were ambiguous; consistent with incipient species in the gray zone of speciation. Overall, this study contributes to the limited but growing body of genetic work on Southeast Asian fireflies and underscores the urgent need to increase the breadth and depth of geographic, taxonomic, and genetic sampling to provide a deeper understanding of their biodiversity and evolutionary history.

evolutionary biology↗

bioRxiv2019

Linking patterns of genetic variation to processes of diversification in Malaysian torrent frogs (Anura: Ranidae: Amolops): a landscape genomics approach

The interplay between environmental attributes and evolutionary processes can provide valuable insights into how biodiversity is generated, partitioned, and distributed. This study investigates the role of spatial, environmental, and historical factors that could potentially drive diversification and shape genetic variation in Malaysian torrent frogs. Torrent frogs are ecologically conserved, and we hypothesize that this could impose tight constraints on dispersal routes, gene flow, and consequently genetic structure. Moreover, levels of gene flow were shown to vary among populations from separate mountain ranges, indicating that genetic differentiation could be influenced by landscape features. Using genome-wide SNPs in conjunction with landscape variables derived from GIS, we performed distance-based redundancy analyses and variance partitioning to disentangle the effects of isolation-by-distance (IBD), isolation-by-environment (IBE), and isolation-by-colonization (IBC). Our results demonstrated that IBE, contributed minimally to genetic variation. Intraspecific population structure can be largely attributed to IBD, whereas interspecific diversification was primarily driven by IBC. We also detected two distinct population bottlenecks, indicating that speciation events were likely driven by vicariance or founder events.

evolutionary biology↗